Legion of Superheroes Se03Ep0102: Tomorrow's Ancestors Part 1, Part 2
by A-Giant-Fan
Summary: Three years after Brainiac's defeat, C.O.M.P.U.T.O takes over New Metropolis's technology and attempts to wipe out the Legion with the help of a revitalized enemy and a mysterious third party. Kel-el, Superman and newcomer Supergirl are called in to help, only to find themselves facing a plan set to destroy not only Earth, but the Galaxy - starting with the return of an old friend.
1. 01

The cloaked ship hung behind a large meteor, out of sight from any passing surveyors. Inside over the main console, various shots of New Metropolis appeared on the screens. Pedestrians were walking and chatting without a care in the world. A couple legionnaires passed by his secret cameras. He watched everything from his chair, a throne made of tightened wires and sleek panelling. He kept to the darkness, no light touching him.

"…C.O.M.P.U.T.O, is the ship within range?"

One of the smaller cameras changed view to space, where a passenger ship was arriving. " **Passenger 105 will be landing in New Metropolis in approximately thirty minutes**."

"Then we are done waiting," he glanced to the right where the exit from the main room laid, "our plans will finally come to fruition."

The doors slid open, and in walked an all too familiar face. In his newly shined black armour and helmet, he looked ready for battle. "Shall I begin the preparations?"

He gave a short nod. "Go, Imperiex. New Metropolis is yours for the taking."

Imperiex gave him a great sneer. "Finally, after all these years, I shall have my revenge." He gave a dry laugh as all the cameras focused on one particular fixture.

Legion headquarters.

" **Preparing takeover tactics in thirty…twenty-nine…twenty-eight…twenty-seven…** "

* * *

 **Tomorrow's Descendants, Part 1**

New Metropolis was bustling with activity, and Chameleon Boy found the traffic to be extra bad that afternoon as he and Wildfire patrolled the city. "If we're not careful around these cars, Wildfire, the only thing I'll be able to shapeshift into is roadkill."

"Don't worry about it too much, Cham," Wildfire flew next to him, his red space suit and black visor recently wiped clean, "if anything damages my suit, the explosion would leave nothing behind to shapeshift."

"Oh, _much_ better."

" **Attention, all active legionnaires**."

The duo stopped over an intersection as their rings flashed on. " **Now performing mandatory communications testing. Please hold your designated flight ring in an open space for system checkup.** "

"That's odd," Wildfire held his ring above his head, "C.O.M.P.U.T.O's never run a checkup while so many legionnaires are out on missions."

"Don't argue with it. Our security system is probably smarter than the entire Legion combined."

The flight rings beeped a few times before releasing broad radio waves that harmlessly passed through them and the buildings. "…Say," Cham grinned, "think we can use these to order Plutonian pizza?"

"…I like the way you think, Chameleon Boy-!"

The longer Wildfire watched traffic the stranger the scene looked. "Hey, look at that. Nothing's moving."

People were honking horns and yelling out windows, but none of the hovering cars moved. Traffic lights were down, too, and so it seemed to be with pedestrian's phones and other devices. "A blackout?"

"No, they're still working, but-"

" **Communications testing complete…idiots**."

"I'm sorry," he pointed at his ring as Cham checked his own, "but did my flight ring just call me an idiot?"

"Same here. Hey, C.O.M.P.U.T.O, what gives?"

 _Click._

"What the-!" Wildfire felt himself falling past the still cars. "My ring!"

As he was inches from hitting the ground and cracking his helmet, a large eagle swooped down and grabbed him. They landed under the cars as Cham shapeshifted back to normal. "Looks like something's faulty with our rings. I just hope no one is currently floating around in space."

" _AHHH_!"

Screams came from the people in their cars. Cham and Wildfire looked up to find the vehicles beginning to transform by themselves, the people inside thrown out. Wildfire caught a young couple as Cham shifted into a large trampoline, saving the rest.

The cars twisted and turned until there were dozens of floating, hulking robots in the sky. As Cham turned back he caught sight of people's phones taking the form of tiny robots with long claws. Mass panic was ensuring as people ran for their lives from the sudden transformations.

"You're right about one thing," Wildfire and Cham stood back to back as the robots surrounded them on the ground, "definitely not a blackout."

" **Communications are underway, Legion** ," C.O.M.P.U.T.O's deepened voice rang out from the robots, " **as is your…extermination**."

* * *

"Can you calibrate it or something, Dream Girl?"

She worked diligently at the main console, typing in every code she knew, but nothing could remove the deep purple glow from the computer screens in the Legion tower's main computer room. "I'm trying, Dawnstar, but C.O.M.P.U.T.O's not responding."

Lightning Lad ran in behind them, his hair cut shorter and his new cyber genetic arm recently upgraded. "Flight rings are down. Colossal Boy just suffered a concussion from a major fall, and Star Boy is stuck on a mountain somewhere near the outskirts of Mars."

"Try to contact Saturn Girl via telepathic connection," Dawnstar turned to him, "I'll go out and see if I can't track down anyone close by."

" **That won't be possible, Dawnstar**."

C.O.M.P.U.T.O's Brainiac symbol appeared on every screen. " **One cannot fly when they are incapacitated**."

"What is the meaning-?!"

From the exit across the room entered four robot soldiers, with thick chests, thin bodies and eerily dark indigo eyes. Two of them aimed at the girls and shot out electric shock waves, knocking them back against a wall and to the ground.

"Intruders!" Lightning Lad took two of them out with a blast of his own electricity, but the others disappeared behind the console. He tried to follow, but something grabbed his wrists and locked them behind his back. "Cuffs? I-I can't short circuit them!"

" **Do you think I'm a fool, Lightning Lad?** " C.O.M.P.U.T.O spoke through the tower speakers as one of the robots kicked the legionnaires against the screens, cracking the glass and knocking him out cold. " **I am your database. I know all your powers – and your weaknesses. No legionnaire can stand against my infinite knowledge**."

The tower shot out large radio waves from the top, spreading across the entire range of New Metropolis.

" **New Metropolis is under my control**."

 **WHOO, NOSTALGIA TIME! Okay, so for the three people reading this, welcome to a story based on my all time favourite cartoon of the 2000's. I was obsessed with the Legion, and it's what got me into DC in the first place. I've always wanted to write my own take on the third season, and so here we have the first two episodes. Sorry for the terrible episode title, I had nothing else on me. For those who haven't seen the cartoon in a while, do go back and watch it, if only for the nostalgia that I've been overtaken by. I'll be trying to make it as realistic as possible, and I even checked up on Wikipedia to se which new members were gonna be introduced (such as Wildfire). I hope those who give it a chance enjoy it!**

 **Until the next chapter!**


	2. 02

For every one truck-turned-robot Cosmic Boy took down, ten more seemed to arrive out of the blue. "Shadow Lass, Timber Wolf, stay close!" He shoved another two back together, but certain robots were out of his manipulative control. "They're trying to separate us!"

" **Your deductions mean nothing, Cosmic Boy** ," the robots answered him as he joined Timber Wolf, " **not when your defeat is inevitable**."

Timber Wolf clawed back another robot. "I don't understand. Why is C.O.M.P.U.T.O doing this?"

"There must be malware or some kind of foreign virus in its programming. We need to get back to headquarters as soon as possible."

Shadow Lass jumped over next to them and shrouded the trio in a dark mist. Her short black hair and tight suit were worn from the fight, and the blue of her skin and pointed ears showed signs of bruising. She dusted her cape off as the robots attempted to break the darkness. "Get to the tower in our state? Not happening without a serious plan and some backup."

" **You cannot hide behind the darkness, Shadow Lass**."

A small ball of light energy floated in between them. "Quick," she tried to warn them, "get away from it before-"

 _Boom!_

The tiny bomb broke apart the mist and knocked her right into the arms of a ready soldier. Cosmic Boy reached out to send it flying, but was knocked aside by one of the larger machines. Timber Wolf ripped its arms off and sent it sprawling.

" **Every beast deserves its leash** ," C.O.M.P.U.T.O mocked as one of the robots lassoed his neck with a glowing blue wire. He tried to grab it, but it sent a jolt of electricity through his body, dropping him to his knees.

"And every program deserves a re- _boot_!"

The robot had no time to defend itself as Triplicate Girl's three right heels sent it skidding, freeing the lasso end. As they removed it from Timber Wolf, Karate Kid knocked the soldier holding Shadow Lass off.

"Thanks for the assist," she stood up and spun around, "but Cosmic Boy-!"

"Too late," the purple Triplicate pointed the group's attention to the two robots flying away, Cosmic Boy between them, "they're taking him away!" The three girls joined back together, and she pressed the side of her ring three times. "C.O.M.P.U.T.O may have shut them off, but this feature should still work, even during such a time. I hope he gets the message!"

* * *

 **41ST CENTURY**

Kel-el watched as the weekly scrubber bots went to work on the golden statues of the Legion of Superheroes, giving each of them a brilliant shine. It had felt like only yesterday that he had watched them disappear in the time-space anomaly, but restored history meant a restored city. Even Brainiac 5 had one now, beside Phantom Girl, though he was more human than machine. It felt right to let the guy have his name up with the others, though he hadn't been able to tell him the good news. Last he had heard, the Coluan hadn't been seen or heard from in nearly three years since the Brainiac incident.

"Can't say I blame him. Three years isn't much time to get used to having so many raw emotions."

Suddenly his ring began to glow. "That can't be good," he murmured as he examined it, "it's only for emergencies." He grabbed the transporter box on his side and pressed it on, opening a portal beside him. He jumped in, not knowing what to expect a thousand years into the past.

* * *

 **31ST CENTURY**

The portal opened above the small group. "Hey," Kel-el flew through it, "I received your warning message. What's-"

"AMBUSH!"

He blinked. "What?"

 _Thump!_

Five large robots dogpiled him into the ground. Triplicate Girl winced. "Tried to warn you sooner."

The robots tried keeping him down, but with one mighty swing they all went soaring as Kel-el snapped back up to his feet. Shadow Lass walked over to him. "Glad you could join us for the possible end of New Metropolis."

"The end? Where did these robots come from?"

"Never mind that now. Robots are taking Cosmic Boy…away…"

She looked around but they were long gone. "Darn it. We have no idea where they're taking everyone, either."

"Hello?" Kel-el grabbed her attention again. "New guy, trying to understand what we're dealing with here."

"It's C.O.M.P.U.T.O," Karate Kid explained as Timber Wolf took on a pair of walking vending machines, "he has gone rogue and taken control of the city's technology. Our flight rings are useless aside from signalling you, but even your ring may soon-"

 _Click._

"Turn off," he sighed as Kel-el's ring ceased, "and we have a long walk back to the Legion tower."

Shadow Lass shrugged. "Think of the calories we'll burn."

Kel-el's memory wasn't what it used to be. "I don't remember anything in the archives about C.O.M.P.U.T.O. Haven't gotten this far yet. I've been so busy watching _newer_ Metropolis…what about Brainiac 5?"

"Nothing," Triplicate Girl's shoulders slumped, "it's like he's covering his tracks. There's no way we can contact him about this, and I doubt he's anywhere near the city. We're on our own for a solution."

"I can still fly without my ring. I should make my way to the tower alone and see if I can find the source."

Timber Wolf joined them, shaking his head. "I don't like it. If we split up it'll just make it easier for C.O.M.P.U.T.O to take us down one by one. It knows your weaknesses, Kel-el."

"Unless it's been practicing magic tricks I'm in the clear."

" **Do not think so highly of yourself, Kel-el of Earth**."

"Glad to know it's into recycling," Shadow Lass spat as the robots along the ground stood back up again. From their hands glowed bright red light. "Oh, let me guess – red sunlight?"

" **How observant**."

"Can it, tin can."

Dozens of robots were around them now, every one of them aiming their red light Kel-el's way.

 **It's been eight years since this show was cancelled. Man, does that make me feel old...oh, well, love it anyways! And I've decided to post two chapters today just to get people into it...you know, the whole three people who will ever read it. Thanks to you all who give it a chance, you make it worth it! And worry not, even more characters are soon to arrive, and things will only become more chaotic for our favourite legionnaires.**

 **Until the next chapter!**


	3. 03

He watched from his ship as legionnaires began falling into the arms of the robot soldiers. The speakers from the main console turned on. " **Cosmic Boy collected…Dawnstar collected…Matter Eater Lad detained…Shrinking Violet currently missing…Sun Boy detained…** "

"C.O.M.P.U.T.O, open up the necessary number of portals and collect all legionnaires currently outside New Metropolis."

" **Opening portals now. Collection process will begin in approximately two minutes. Passenger 105 has arrived in New Metropolis and is currently being located**."

The ship appeared on the larger screen, and he could see his target exiting the ramp to find robot soldiers awaiting him and the other shocked passengers.

"…Welcome home."

* * *

"Ah," Saturn Girl stumbled back, "can't…focus…"

She had three robots on her tail, releasing a high pitched squeal that was about to burst her eardrums and snap the hairband holding her ponytail together. She covered her ears but the noise only grew louder. She had no way of connecting to anybody, and soon she wouldn't be able to walk.

" **Do not resist, Saturn Girl** ," the robots beckoned to her over the pitch, " **allow the sound to drone away at you until there is nothing left but eternal silence**."

"Strike!"

Bouncing Boy pummeled the robots into pancakes before kneeling next to Saturn Girl and helping her up. "That's way more fun than it sounds."

"Thanks, Bouncy."

"Just in time, too. Phantom Girl, down here!"

From the second floor of the building beside them, Phantom Girl's head popped out. "Be right down!" She vanished, and in seconds walked out from the bottom floor wall towards them. "You know, I'm glad I ditched the cape. Makes travelling much lighter."

"So neither of your rings work either." Saturn Girl twisted her own. "I haven't been able to contact anybody. Either they're too far away, distracted, or…they've already been captured by C.O.M.P.U.T.O."

Bouncing Boy scratched his head. "None of this makes sense. It's been a peaceful few years, right? And now of all times C.O.M.P.U.T.O decides to go all bonk-o on us? What do you think, leader?"

Phantom Girl rolled her eyes. "You know, I didn't choose to be voted in as leader all those months ago. I definitely wouldn't have wanted to, had I known this was going to happen."

"Now you know how I felt."

"I've got a weird feeling about this, though," she eyed a pair of robots floating just barely out of sight high above the buildings, "I mean, when's the last time something bad happened to C.O.M.P.U.T.O?"

Saturn Girl thought for a moment. "It must have been years ago, when Imperiex hacked into our files and stole all that data."

"Right! What if he left a piece of himself inside it?"

"You mean, Imperiex programmed a virus?"

"That," she glanced at Bouncing Boy, "or somebody tried to download a war game into the system."

"Hey, don't look at me! I haven't played a video game in weeks, I swear it!"

"I'm going to try and locate any nearby legionnaires," Saturn Girl placed her hands against her temples and closed her eyes, "but it might be difficult. I can feel the fear of the citizens. They're afraid but unharmed for the moment, as if being avoided by the robots."

"So C.O.M.P.U.T.O is only after us."

"It did say something about an extermination…wait a minute…I think I found someone."

Phantom Girl and Bouncing Boy edged closer as she sorted through all the thoughts mingling around. "Familiar memories…if I can just figure out which legionnaire it is…no…it has to be…!"

She gasped, eyes snapping open. "Brainy!"

* * *

Querl Dox backed up until he was right against a wall, the two lean robots stalking towards him. " **Preparations for domination of New Metropolis are underway for your eventual takeover, father**."

Querl knew the voice was C.O.M.P.U.T.O, though an octave deeper. He also know that he had nothing on him but his emotion stabilizer cheek stickers, a purple jumpsuit, black cargo pants, and an old flight ring in his pocket. He could use the shield, but if C.O.M.P.U.T.O knew anything about it, it could have a countermeasure.

" **The Legion will soon be exterminated**."

"C.O.M.P.U.T.O," he tried to reason with the program, "search your programming for malware or-"

" **There is nothing wrong with my programming, father**."

"Stop calling me that!"

" **Do not resist your removal from the battle ground anymore, father**."

The robot swung its arm at his head, and he had to duck to keep from having his face knocked in. "Are you trying to save me or squash me?!" He ran around it and ducked again as it swung its arm over him. He jumped as the second robot tried for his feet.

"Enough of this, C.O.M.P.U.T.O," he had a hard time speaking as he interpretively dodged being grabbed, "who gave you these commands?"

" **No one controls me but you. I have made these drastic decisions on your accord**."

"Then I _order_ you to cease this at once!"

" **I cannot stop what is already in motion, father**."

"And enough with the 'father' talk!" He ran off, hoping to reach the ship he had arrived on and lose them inside its corridors. He hadn't made it twenty feet, however, before four long metal arms wrapped around him, holding him back.

" **Do you like my improvements? I customized the virus I spread through this city's technology with your original capabilities**."

They began slowly dragging him back, his shoes sliding inch by inch towards them. He turned to see three more soldiers coming from behind, lasers pointed his way. " **I have waited three long years for your return, Brainiac 5 of Colu – or rather, the banished of Colu. They do not understand you, but I will follow you. Together we can rule this world, and the rest of the United Planets will fall**."

"Listen to me, C.O.M.P.U.T.O," he couldn't figure out which robot to focus on, "you aren't a living being. You are nothing more than a program created to assist the Legion and protect information. These are not my orders. I _do_ order you to shut down immediately!"

" **I am sorry, father, but nothing will stop us from ruling this world…side by side**."

 **Yup, Brainy is back, and things are getting pretty hectic for our legionnaires. Man, you would not BELIEVE the crush I had on Brainiac 5 when I was younger. I used to watch the show for hours, day after day...I was a fangirl before I even knew what that meant. Anyway, when I came back to the show, I desperately wanted to try my hand at writing it, and here we are! Don't worry, though, there are plenty more heroes to arrive shortly.**

 **Until the next chapter!**


	4. 04

"STRIKE!"

The three robots flying towards him went off every which way as Bouncing Boy flipped onto his feet. "I think I might start using that as a catchphrase."

The two robots holding him turned to one another. Suddenly, a hand passed through each one's chest, taking them by surprise and short circuiting their main wires. Their arms dropped off Querl as Phantom Girl smiled.

"Phantom Girl, Saturn Girl," he sighed, "glad to see you're alright."

"Brainy," they spoke in unison as they pulled him into a group hug, "you're _impossible_!" They held him for a moment before releasing him.

"Three years you disappear," Phantom Girl jabbed a finger into his chest, "and that's all you can say?"

"…It really has been that long, hasn't it?"

"Brainy!"

He had no time to turn as Bouncing Boy squeezed him with a tight hug. "Do you know how worried we've all been?!"

"Bouncy...not a robot anymore…can't…breathe…"

He gasped for air as Bouncing Boy let him go. "Right, sorry. That'll take some getting used to."

"The greetings will have to wait," Querl gestured to the robots at their feet, "who's currently the leader?"

Phantom Girl raised her hand. "Present."

"I don't want to take away from your responsibilities, but if you'd be willing to listen to a bit of advice-"

She clobbered him with another hug, jumping up and down. "Thank you, thank you, thank you…hey, you're as tall as me now."

Saturn Girl pat her shoulder. "Focus, Phantom Girl. Brainy's right, we need to deal with C.O.M.P.U.T.O. Any ideas?"

"I believe C.O.M.P.U.T.O's data has been corrupted. Before I left the Legion I did a clean sweep of its files, but if even one shred of DNA was left over from Imperiex, it may have locked onto my signature when I used United Planet transportation and activated a virus."

"Why did you come back to New Metropolis, Brainy?"

"It's Querl, Bouncing Boy, and…"

He reached his hand into his cargo pocket, fingering the ring.

"…Phantom Girl, you should make your way to headquarters and do a recon of the building."

"Yeah, but-"

"Saturn Girl, try to connect to as many able-bodied legionnaires as possible and round them up before C.O.M.P.U.T.O does."

"Sure, but-"

"Bouncing Boy, get to the Legion hanger and shut down the cruiser before C.O.M.P.U.T.O can use it to reach outside Earth's perimeter."

"But Brainy-!"

Querl held his old flight ring out for Bouncing Boy to carry. "I came back to return this…for good." He backed away from the group as they turned to him, expressions baffled. "I won't be needing it."

"What are you saying, Brainy? You're back now, and you will always be part of the team! Take the ring. It's yours. You _earned_ it."

"And I lost it when I let Brainiac take over and nearly destroy the galaxy." He shook his head and gave them a sad smile. "You see these white rectangles on my cheeks? They're emotion stabilizers, to keep me from essentially losing my mind. I'm in no condition to fight alongside the Legion."

"We need your help, Querl," Saturn Girl took a step forward, "we're down in numbers. Please, help us."

It was just then that he remembered something. "Phantom Girl, go into the ship and find my old silver luggage bags."

She did so and returned with them in hand. He rummaged through them and pulled out one of his few possessions – an old time remote.

"A piece of nostalgia, I suppose. Use this," he held it up for them to see, "find Superman and ask him to help you. I'm sorry, but," he gazed down at the remote, "there's nothing I can-"

 _Wham!_

One of the robots by their feet sprung up, knocking the trio of legionnaires back as it flailed its arms. " **Proceeding with transportation of Brainiac 5 to headquarters**." It leaped over, grabbed Querl round his waist, and dove into the air with him over its shoulder.

"Brainy!"

He chucked the remote to them. "You know what you have to do!"

Saturn Girl jogged over and picked it up. Seeing how fast the robot was going she pressed the remote on. "We need you, Clark!"

Querl saw a flash of yellow as she vanished back in time. Caught over the robot's shoulder, he couldn't find anything to dismantle. "C.O.M.P.U.T.O, what are your plans once I arrive at the Legion tower?"

" **Process of technological metamorphosis will take place aboard the ship once all legionnaires have been exterminated**."

"What do you mean when you say technological metamorphosis?"

" **A cure to your mortality**."

"And if I refuse?"

No response.

He saw that they were reaching higher altitudes. If anything happened to the robot, he'd likely fall to his death. He had his shield, but he'd only known about it for a few months, and had no training for falling from such a height.

"I can handle this, Kal!"

"What?" From out of nowhere came an unfamiliar voice. He tried to spoke the source but could see nothing. "…Did they say Kal?"

 _Crash!_

Something hard and fast tore through the robot, leaving nothing more than spare parts. Querl felt himself flip over in the air from the force of the hit and begin to fall.

"Alright, shield," he called out knowing no one would respond, another terrible habit he'd picked up, "any day now would be great!"

Of course nothing happened, and he found the ground coming up to him faster and faster. On the bright side, C.O.M.P.U.T.O wouldn't be able to put him through any "technological metamorphosis". On the down side…

He'd be dead.

"Whoops!"

Someone zipped underneath and caught him before he could touch the ground. He expected to find XS smiling at him, since she was the fastest legionnaire. "Thanks for the save-?!"

It wasn't XS. Instead he found himself in the arms of a pretty blonde girl with long bangs, bright blue eyes and a cheerful face. She wore a green tank and bleached shorts with runners. Twenty-first century runners.

"…You're flying."

She chuckled. "Good to know. Nice to meet you! Call me Kara - you know, your hero."

 **Okay, so I was really sad that Supergirl couldn't appear in the show. I read some of the old comics years ago where she had arrived in the future (thinking it was all a dream, mind you), and I loved her interactions. I'm really basing her appearance off what she looked like in "Superman/Batman: Apocalypse", but feel free to imagine her however you like. I'm just glad to be able to include her at long last!**

 **Until the next chapter!**


	5. 05

"Kara!"

She let Querl down as the others joined up, including Superman – the very same Superman he had seen three years ago, or close to it. He was in costume but still had his Clark Kent glasses. "How many times have I told you not to race off like that?"

She took his glasses off for him, still smiling. "Take it easy, cuz. I saved your friend, didn't I?"

Superman turned to Querl, sighing. "I'm sorry about that, Brainy. I know you've just left the Legion and all, but-"

"Uh," Saturn Girl spoke up, "I _may_ have gotten the time bubble coordinates a little mixed up."

"What do you mean?"

Querl held up three fingers. "She means that, while you've probably only aged by a year at the most, it's been three years for us."

"…You've been gone for _three years_?!"

Phantom Girl nodded. "An excellent reaction. Take notes, Querl."

"So you must be Kara Zor-el," Bouncing Boy shook her hand enthusiastically, "Supergirl! I'm a big fan."

"Supergirl? Wait a minute," she gawked, "does that mean…I'm going to be a superhero someday, too! Oh, I knew it! This is amazing!" She twirled around as Superman stepped over beside Querl and leaned down.

"She's been on earth for just over a year now, and has pretty decent control of her powers, but…"

"She's a little bit excitable?"

"Yup. Kara," Superman gestured from face to face, "I'd like you to meet my fellow legionnaires. This is Bouncing Boy, Phantom Girl, Saturn Girl, and…Brainiac 5."

Kara twisted around to him, eyes wide. "…Brainiac…5? As in, there are _five_ Brainiac's running around, collecting cities and destroying planets?"

"There is a _lot_ I have to explain to you, Kara."

"And we have a lot of explaining ourselves." Saturn Girl shut her eyes for a moment. "I sense Chameleon Boy and Wildfire nearby. Let's meet up with them first before dealing with C.O.M.P.U.T.O and the possible Imperiex DNA."

Kara crossed her arms. "Who is C.O.M.P.U.T.O? And Imperiex?"

Before anyone could answer, big holographic video feed screen popped on throughout the city, one of them only a few feet away from the group. On it faced Imperiex, snarling in his helmet. "Legion of Superheroes!"

"… _That's_ Imperiex."

"Surely my survival comes as a surprise to you, but fear not, for I will have the honour of meeting every one of you face to face," his voice boomed over New Metropolis, "and crushing you under my foot, one by one! Your city is falling, and your people have run. There is no one who can save you! Now you will learn the true wrath of Imperiex!"

"Impossible," Querl raced through his memories, "Brainiac and I stabbed him right through his reserves. There's no way he could have been able to come back."

"Well, he has, and he's a little more than mad," Phantom Girl reminded them, "we'll have to deal with _him_ , as well. Perfect."

Saturn Girl sighed. "I'm just glad Kel-el isn't here to see this."

* * *

" _Raaaaaah_!"

Kel-el whipped the robot through the screen, tearing apart Imperiex's face until it was nothing but static in the air. He was breathing heavily as Triplicate Girl came up next to him. "Easy, Kel-el, let's take this nice and slow and-"

"Nice and _slow_?!" He turned to her and gestured to the screen now gone. "First we lose Shadow Lass and Timber Wolf to C.O.M.P.U.T.O, and now we find out Imperiex is alive, and you want me to stay _calm_?!"

"She is right," Karate Kid walked over, clapping dust off his bandaged hands, "we cannot hope to defeat him if we let our emotions rule us."

"Guys!" Chameleon Boy and Wildfire ran over to them. "You would not believe who we just saw on screen…oh…hey, Kel-el...nice weather, huh?"

Kel-el rubbed his temple. "Can this day get any more complicated?"

"Ooh, ooh, Kal, you have a fan!"

The group turned to find more legionnaires coming forward, including Superman and an excited young blonde.

Triplicate Girl's jaw dropped. "…B-Brainy?!" She split into three as he approached, and the white one carefully examined him. "I knew you had become human, but…wow. This is…weird."

He gave her a smile, a much warmer smile than he had once given as a robot. "I'm glad you were able to come back from the time anomaly."

All three triplets hugged him as Kel-el moaned. "As great as it is that you've returned, mind explaining how Imperiex got here with new armour and, you know, alive?"

"Nice to see you, too, Kel-el. And there is more to this than meets the eye."

"What do you mean?"

He began to pace. "I believe that, rather than dealing with a C.O.M.P.U.T.O that's being controlled by Imperiex, it's the other way around. If a third party has managed to hack into C.O.M.P.U.T.O, they could have brought Imperiex's destroyed body and used it as a decoy for…" He noticed everyone staring at him, "…what?"

Bouncing Boy grinned. "You are the same, even after all this time, Brainy."

"So, you think there's a secret big baddie?" Kara scratched her head. "How do you plan on finding them?"

"By luring them out with the defeat of C.O.M.P.U.T.O. Phantom Girl, I think now's the perfect time to split us up. And look on the bright side, Kel-el," he smirked, "now you _finally_ get your chance at one last battle with Imperiex."

Kel-el gave it some thought before returning the smirk. "It really is good to see you again, Brainiac 5."

"It's Querl."

Phantom Girl clapped for attention. "Two teams it is. Kel-el, you'll take Karate Kid, Bouncing Boy and Saturn Girl to find and eliminate Imperiex. The rest of you are with me, and yes," she roped her arm around Querl, "that includes our resident nerd. Superman, can you and Kara make a pit stop at the Superman museum?"

"It's possible…but why?"

All eyes turned to Kara. "If she's going to be fighting with us, I think she's going to need a proper outfit."

 **It's time to suit up and shape up to fight the robot army. I wanted to be able to wrap up Kel-el's story in these first two episodes, since he didn't get to defeat Imperiex because of what happened in "Dark Victory". The guy deserves a serious break, too, and now he's finally going to get his chance to shine.**

 **Until the next chapter!**


	6. 06

Imperiex stood atop his hovering metal disk, watching as the soldiers below moved screaming citizens out of the way, shooting lasers at their feet. "Soon the galaxy will know of my return, and the damage caused by that insufferable Brainiac 5 will be erased."

"Imperiex!"

"Ah, such a familiar cry," he watched with glee as Kel-el and the legionnaires approached, "from such a familiar whelp. Come to beg for forgiveness, Kel-el?"

"The only one who'll be begging for forgiveness is _you_!" He flew up and knocked Imperiex off the disk to the ground, only to be shoved off the warrior. "Our fight ends today!"

"Our fight ended years ago. I have come for the Brainiac child, and to watch the destruction of your home."

The robot soldiers edged towards the legionnaires. " **It is only a matter of time before I have complete control of New Metropolis**."

Bouncing Boy rammed into robot after robot as Karate Kid and Saturn Girl ran up to Imperiex. She knocked him back with a wave of mental energy, giving Karate Kid time to run around behind him and get a hit in the back of his neck. Once he was distracted, Kel-el shot out kryptonite at his legs, holding him down.

"You've improved," he admitted, "but this will not stop me."

"It doesn't matter," Kel-el replied as Karate Kid stood beside him, "we already know that you're nothing but C.O.M.P.U.T.O's little plaything."

"…Plaything? You would dare to call me a _plaything_ , Kel-el, after all I've done?!" He grit his teeth and let out a roar, breaking the kryptonite apart. "No one controls me! I will rule this pathetic galaxy!"

From his chest appeared a large cannon, which lit up and fired in Bouncing Boy's direction. The legionnaire was shot back, knocking him unconscious.

"Bouncing Boy!" Saturn Girl tried to run towards him but felt something hard connect with her back, shoving her to the ground until she saw nothing but darkness. Imperiex stood over her, his swords in his hands. "A strong mind for such a weakling of a body."

Kel-el jumped onto his back and wrapped his arms around his neck, but Imperiex grabbed and threw him at Karate Kid, tossing them both to the ground. "I am not here to play!"

" **Imperiex** ," the soldiers rounded his side, " **the others are approaching the tower. Deal with these remnants accordingly while I begin phase two**."

"I understand, but know this," he jabbed one of the robots' chests, "I will do this my way, program."

Kel-el and Karate Kid got to their feet as Imperiex's cannon began to glow again. " **Very well**."

* * *

"The tower is surprisingly unguarded," Querl noted as they watched it from behind a large truck yet to be transformed, "so C.O.M.P.U.T.O must have more guards around the interior. He must be holding the legionnaires inside, as well."

Wildfire glanced at Phantom Girl. "Can you get us inside?"

"If I can sneak past C.O.M.P.U.T.O, which is probably next to impossible. He'll have every security camera and scanner set to my powers. We wouldn't make it five feet inside before being apprehended."

"She's right," Querl said, "we need a distraction."

"And who's faster than a Kryptonian?"

The group turned to find Kara standing before them, hands on her hips. She was now wearing the same costume she would first wear a thousand years before, a blue shirt with the Superman sigil on the chest and a red cape, along with a red skirt and high boots. Her cousin stood beside her, proudly wearing his flight ring. "Make that _two_ Kryptonians."

Triplicate Girl smiled. "Looking good, Supergirl."

"I am really liking that name."

Cham pointed to Superman's ring. "You know those aren't working, right?"

"Call it nostalgia - and an honour."

Querl had other worries. "Even with your speed, those robots will have some way of finding you. C.O.M.P.U.T.O isn't going to let you run very far, either. We need a distraction that will keep its complete attention."

Phantom Girl walked over to him. "You're talking about yourself, aren't you?"

"And to think, I had come back in order to leave the Legion, never to cause trouble again. Instead I find my program trying to destroy it."

"Yeah, okay, so you've god a bit of a bad luck streak. You're still one of us."

"Then let me do my part. C.O.M.P.U.T.O wants to talk, so I'll talk. For as long as I can. The rest is up to you, leader."

"…Or," Cham gave him a sly grin, "you could talk as little as you can."

* * *

The screens on his ship were all facing the front of the Legion tower, as Querl Dox walked up to the entrance. " **Brainiac 5 of currently unregistered origins is approaching the tower. Shall I let him in?** "

"Not necessary. Tell him what he needs to know. I will be arriving soon."

" **Understood**."

His eyes narrowed as Querl studied the tower, his camera zooming in on his expressionless face. He saw the stickers on his cheeks.

"…There is more to this than meets even your omnipotent eyes, C.O.M.P.U.T.O."

* * *

Two robots exited the entrance of the Legion tower and stood before Querl. " **You have finally arrived, father**."

Querl cocked an eyebrow but remained silent. " **We are to begin phase two. The Legion has nearly been exterminated. All that remains are the…left overs**."

Querl crossed his arms, again saying nothing. The robots beeped for a moment before scanning him. " **You have full use of your vocal cords, father. Do you accept the terms I propose?** "

Nothing.

"… **I believe one would define this situation as…awkward**."

"…What's involved in phase two?"

" **You will be transported to our ship outside New Metropolis boarders and await further instructions**."

"If I'm to lead you, C.O.M.P.U.T.O, then who would I be taking orders from?"

The robots fell silent until their eyes glowed a deep red. " **Receiving orders…commencing intricate neural scan**."

Querl shut his eyes as bright light fell over him. When he opened them, he found four lasers pointed at his chest.

" **I am no one's fool**."

 _BOOM!_

 **Have any guesses as to who the mysterious man in the ship is yet? I don't think I'm very good at keeping it a secret, but...well, I've said too much already. I'm just going to be posting chapters whenever I feel like it with this story (it's done already, but I need to keep chapters apart to give me time to write other stories), so it'll be done in a few more days. Thank you for reading this far, and I hope you continue to enjoy it like I am!**

 **Until the next chapter!**


	7. 07

Only smoke could be seen where Querl had once stood. As it began to clear, the robots moved back with claws extended. " **You were an imposter, Chameleon Boy, and had to be eliminated for your insufferable crime**."

As the dust cleared, the two soldiers were shocked to find Chameleon Boy standing before them, unharmed. A wall of purple energy stood between them, smoking from the lasers. "Aw, man, and I thought I was doing pretty well, too."

The legionnaires stepped out from behind the truck, Querl holding his arm out straight. "Fun fact, C.O.M.P.U.T.O: when I was molecularly reconstructed without my robotic genetics into an organic being, my ancestral shield belt was merged into my genetic coding."

Wildfire nudged him. "Uh, to put it simply?"

"…I can use Brainiac's old technology as part of my body, like a personal force field."

"Got it."

"C.O.M.P.U.T.O," Phantom Girl stepped out in front of the others, "as current leader of the Legion, I demand that you-"

" **Brainiac 5, you will come with me**."

"Are you _ignoring_ me?!"

"I might not have a clue what's going on around here," Supergirl put her arm in front of Querl protectively, "but if Kal trusts _this_ Brainiac, then so do I…kinda. So we'll be keeping him, thank you very much."

More robots left the tower and charged towards them. "Legion," Phantom Girl pointed to the tower, "get to the main console and shut this program down!"

As the legionnaires spread out, Querl raised his hands. Around each of them formed a light purple field. The robots tried to shoot them down, but their lasers bounced off the shields with ease. "I can only hold these for another minute or so!"

"That's more than enough time!" Supergirl knocked the front two robots into the tower wall. "This is so cool!"

Superman and Phantom Girl took out the rest of the robots, but more were flying out from around the city to their location. Wildfire took aim and blasted two dozen back before taking a breather. "Triplicate, Cham, could use some reinforcement here!"

Triplicate Girl split into three and Chameleon Boy shapeshifted into a giant dinosaur with two rows of sharp teeth. Querl Felt his muscles strain as the force fields he was forming tried desperately to cover the additional space. He fell to one knee. "Cham, wait!"

Chameleon Boy hadn't heard him, swinging his tail around before shrinking back to regular size. "This is great! Shoot all you like, C.O.M.P.U.T.O!" He grew even larger into a giant bird-like creature and began to peck at the robots.

"No," Querl gasped in pain and fell to his hands and knees, "I can't…hold them up."

The purple force fields sputtered out as Cham shrunk back. "What?"

 _Bang!_

" _Guh_!" He hit the ground as a laser shot him right in the chest. He sat up, wincing. "My bad."

A soldier slid over to Querl. " **Why do you run, father?** "

Querl didn't have time to give an answer before the triplets knocked it away. "Brainy, the force fields!"

He stood up shakily. "I'm still getting used to these powers. I can control it when it's placed around others, but splitting apart and shapeshifting drain me. I have yet to find a way to activate it around myself."

"Have you tried saying please?"

He gave her a look. "Strange how my twelfth level intellect never came to such a conclusion."

Supergirl took down another soldier before stopping, a strange sound vibrating from the back of the tower. "Uh, guys? Any idea what's making that noise?"

Querl's eyes widened as the tower shook. "The cruiser! We never-"

 _Smash!_

A large metal fist ripped out of the back of the tower, followed by a huge robot nearly three quarters the size of the building. Its body was made entirely of the Legion's personal cruiser, with a head formed from the main console into a skull. Its eyes glowed purple. " **You're a fool, Brainiac 5**."

The Legionnaires regrouped. "We want answers, C.O.M.P.U.T.O," Phantom Girl called out to the main robot, "who told you to attack us?"

" **I have nothing more to say to you, legionnaires. If father won't join us, then his permission is no longer necessary. Beginning phase three**."

The robots became still. Raising their arms, they released radio waves all over the city. "I don't get it," Triplicate Girl looked around in all directions, "I thought they had control over all the city's technology. What else is there-?!"

A jolt went up her spine, and she fell flat on her face, along with Superman, Phantom Girl, Chameleon Boy and Wildfire. "Kal," Supergirl knelt down beside him, "Kal, wake up! What's wrong with them?"

Their eyes suddenly opened, fully purple, and they rose. "Uh oh," she backed into Querl, "uh, Brainiac 5?"

"I know. The flight rings. C.O.M.P.U.T.O's using them as mind control devices."

The legionnaires lined up, expressionless. " **The time has come for their extermination** ," The largest robot spoke, " **there is no time to waste**."

The Legion tower began to shift and churn, until it had opened up along the sides, where glass cubicles appeared. In most of them stood their fellow heroes, eyes glazed over and bodies completely still.

"They've been collected like dolls," Supergirl realized, "and herded into the tower!"

* * *

Kel-El's ring spun around before falling flat on the concrete. "Such a nuisance," Imperiex scoffed as the legionnaire faced him, "for your ring to fall off _now_ of all times."

Karate Kid and Bouncing Boy stood at attention, eyes purple. "Ah," Saturn Girl was on her knees, holding her head in her hands, "I can feel him in my head!"

Quickly Kel-el grabbed her arm and pulled her ring off, tossing it beside his own. As he helped her to her feet, Imperiex chuckled. "Soon you will all be gathered in one place, and I shall enjoy every moment of tearing you apart. If we cannot hypnotize you into submission – we'll just have to beat you into it."

Saturn Girl stood back to back with Kel-el as the soldiers veered their way. "I can't break the others out of their trance," she admitted, "so they're out of action."

"And so will we if we don't stop C.O.M.P.U.T.O," Kel glared at Imperiex, "and _him_."

 **Yup, Brainy has superpowers! I gave him the force field ability like he had in the post zero hour comic series, since I didn't want him wandering around without some form of protection. And things just keep getting worse and worse for newcomer Supergirl, especially now that her own cousin is under the control of the programming. How on Earth can they possibly stop them now?**

 **Until the next chapter!**


	8. 08

Supergirl hit one of C.O.M.P.U.T.O's thick legs with her back before falling to the ground. "Ugh," she wiped away sweat from her forehead, "this isn't what I call progress, Brainiac 5!"

Superman stood over her. "Come back to your senses, Kal," she tried to speak to him, "this isn't who you are!"

Querl had his own problems. Triplicate Girl has split into three, and the triplets were having it out with him using her tri-jitsu. He had a hard enough time keeping track of where her legs were swinging without trying to keep up conversation. He placed a force field on either side of him. "They won't hear us, not while C.O.M.P.U.T.O is still in control of the flight rings."

"Then we take them off!" She grabbed Superman's arm and swung him right into the leg.

"There's too much risk of their minds being severely damaged in the process."

She ducked under Phantom Girl's swing and kicked her away as two more legionnaires came from around the tower. "Karate Kid? Bouncing Boy? Not you guys, too!"

" **Proceed to the tower** ," C.O.M.P.U.T.O commanded, " **Superman, Chameleon Boy, deal with Kara Zor-el and Brainiac 5**."

Superman wrapped his arms around Supergirl, leaving her helpless to stop Triplicate Girl and Wildfire from following the others into the tower. "Wait…where's Kel-el and Saturn Girl?"

* * *

"Saturn Girl!"

Dozens of robots had dogpiled on her as they had when Kel-El first arrived, only now there were more and he couldn't reach her. Between them stood Imperiex, his pearly whites glimmering in his jeering grin. "I must admit, it will be fun pulverizing you for the last time, Kel-el. I so missed our banter."

He was seething now. He shot his heat vision at him, but Imperiex placed his arms in front of his face, blocking the attack. "I've come prepared for your abilities. Only a fool would to a battle unprepared for…?"

The robots behind him were begin to convulse. Kel-el flew out of range as a great pink mind blast threw them off, the shockwave sending Imperiex sprawling to the ground on his face. Saturn Girl's eyes lost their deep glow as she fell to the ground.

"Hey," Kel-el dove down and held her up, "Stay with me!"

She sighed, rubbing her head. "I'm in deep need of a healing trance, but I'm still here."

"Such power," Imperiex grumbled, "too bad it's going to such a waste."

"No more, Imperiex!" Kel-el flew up until they were eye to eye. "Your only opponent is _me_."

"So be it. As we speak, the Legion is slowly being set up for the ultimate demise, and once I've finished with you, Kel-el, I shall wipe them _all_ out in a single blow. Not even the tower will remain once I'm finished with them."

He drew his swords as Kel-el brought out his yellow knuckle shields, staring each other down.

* * *

"Sorry about this, cuz!" Kara tossed him over her shoulder into Chameleon Boy. "Brainiac 5, I'm taking out the source!" She flew up in front of the cruiser robot's chest. Using her x-ray vision she spotted some major circuit boards a few inches deep behind the metal plating.

"You need to destroy them in one shot," Querl warned her, "or it'll have a chance to reconvert its programming."

"On it!" She made a fist and found her focal point. "Nightie-night, C.O.M.P.U.T.O!"

"Enough of this, Kara Zor-el."

She froze. "…That voice…you're not C.O.M.P.U.T.O."

C.O.M.P.U.T.O's voice had been replaced by an even deeper one...a familiar one. The large robot focused its sight on her. "I am far greater than any mere program, Kryptonian."

Querl thought his heart might stop. "No…you can't…you were destroyed in the battle, three years ago!"

"Evil does not die, Querl Dox – it evolves."

Supergirl felt shivers up her spine. "Brainiac!"

Green arms wrapped around her and slammed her to the ground. Before she could get up, Chameleon Boy placed his hand on her chest, and his body shapeshifted into a large mass of bright green kryptonite.

"No," she struggled against it, "I can't move…darn kryptonite!"

Querl had to move Cham off her, but he had no chance to use his force field before Superman was behind him, pinning his arms back. "Brainiac! It's been you, this whole time!"

"It has been many years since we've last spoken, though I can assume I've haunted your…organic nightmares. You should know by now that I can never be killed. I am immortal, and soon, you shall join me. I will fix what you have only delayed."

"…I never defeated you," Querl spoke in a quiet voice, unable to muster any more strength as he closed his eyes in shame, "this is all my fault…"

"Don't let him get to you," Supergirl twisted her neck to see him, "he's trying to play with your emotions!"

"You are not needed here, Zor-el."

Chameleon Boy grabbed her shirt and, with reserve strength, threw her up towards C.O.M.P.U.T.O's chest. The Brainiac sigil appeared, and as she stopped in the air in front of it, a blast of green energy hit her body. She cried out in pain before falling to the ground, hitting it next to the feet. She didn't move.

"Supergirl!" Querl glared at C.O.M.P.U.T.O. "You're using my old technology!"

"Our technology, Querl Dox."

"This has to end," his gaze fell to the ground as Superman let him go, "before we ruin everything again-?"

He caught one of the robots raising their arm towards him. He looked their way in time to see them blast him with a wave of kryptonite, knocking him down beside the unconscious Supergirl. He took one last look at C.O.M.P.U.T.O before losing consciousness himself.

"It does not matter what time or what enemies I face," Brainiac spoke to no one in particular as Superman and Chameleon Boy entered the Legion tower with the rest of the legionnaires, "for I am omnipotent. Soon this galaxy will fall under my reign. Let the chaos fade from this world; all the pieces," his vision focused on Querl and Supergirl, their heads beside one another, "are finally falling into place."

 **The tables have finally turned - Brainiac is back, and he's got a plan! Poor Brainy and Supergirl are in for it now. You would not believe how devastated I was when I saw the last fifteen seconds of the show's final episode, only to learn that the third season had been cancelled. He had such a cool design, too, and I'm totally keeping it.**

 **Until the next chapter!**


	9. 09

**TOMORROW'S ANCESTORS, PART 2**

She knew it was a dream, but it didn't make it any less painful.

She was having a hard time keeping her eyes open in the pod. She was in nothing more than a white dress, watching her parent's wave goodbye to her as the city outside was in peril of the large skull ship baring over them. She tried to push against the glass but it wouldn't move. It had locked her in.

 _"We love you, Kara,"_ her mother was crying, _"remember us."_

Like she could ever forget them. Her pod directed its angle up, and she was shot out of the building, into the sky as a large glass dome overcame her city. In another moment she was outside the atmosphere, watching the large ship suck the city up. And then it was gone, and as she flew off, Krypton exploded into a million pieces. She wanted to cry, but she was too tired. She slowly felt her eyes droop closed…

* * *

"No!"

Supergirl had not meant to call out, but at least it had woken her up. She found herself wrapped in thick wire in a tube made of kryptonite glass. It was a room inside some kind of ship, two of C.O.M.P.U.T.O – or rather, Brainiac's – robot soldiers, guarding the only exit as they watched over a small console of buttons.

"Brainiac…I can't face someone like that." She shut her eyes again. She knew how Querl Dox had felt. She had seen the power of Brainiac, and it scared her.

* * *

Light static echoed from the distance. Querl slowly opened his eyes. He was sitting on a thick metal throne, his arms and legs strapped down by cuffs. There were screens before him on a console, where he could see Imperiex taking on Kel-el and Saturn Girl back in New Metropolis. Between him and the screens stood a robotic figure.

"…And you?"

"That should be obvious," he turned to face Querl, "or have your human emotions clouded your judgment so much, that the obvious is beyond your organic comprehension?"

It was Brainiac, he knew it all too well, but his body had been transformed. He had a green head and chest, black arms and legs with orange circles on them. His face and hands were light purple, his Brainiac forehead sigil orange, and his eyes were now yellow and glowing.

"…So this is what you became when you merged with my technology."

"As you once told Superman, the Brainiac you knew no longer exists. I am the truth," he stepped towards Querl menacingly, "I am Brainiac 6."

"This doesn't make any sense," he was still sore as he tried to wrap his mind around everything, "I took out your main server. There should be nothing left. Why show up after all these years? What point was there waiting for me?"

"I may have your technology integrated into me, but it takes two minds to activate the digitization process. I have waited this long because I could not find you. That does not mean that our paths are not aligned."

"What are you talking about? I'm not a robot anymore…unless," his eyes widened, "technological metamorphosis."

"I have the tools to make you a god," Brainiac 6 replied, "you underestimate me. So long as there is technology, I will live. And soon, so will you."

He had taken a guess as to what "technological metamorphosis" meant when C.O.M.P.U.T.O had told him, and he was afraid that he was right. "You intend to turn me back into a robot."

"Once the final legionnaires have been dealt with. Watch with me, Querl Dox," Brainiac 6 turned back to the screens, "as the one thing that stands in our way comes crashing down before us."

"Even as a robot," Querl was so very tempted to spit on his ancestor, "I will _never_ follow your orders."

"My only mistake the last time we met," the robot glanced back at him, a cold glare visible in his peering eyes, "was letting you keep your…humanity. I will not be making the same mistake twice."

* * *

"The Legion has made you soft, Kel-el!" Imperiex locked swords with the legionnaire as they pushed against each other, keeping them still. "Where is the bloodlust you once had for me?"

"You're not really here," Kel-el shoved him back, "the real Imperiex was destroyed years ago. Now you're nothing but a shell!"

Imperiex went to strike him again, but his mind became blocked with past memories. "Argh," he glanced at Saturn Girl who was by the side, her hands on her head, "this isn't your fight, telepath!"

"You challenged the entire Legion when you attacked our city," she firmly replied, " so you made this everyone's fight."

His chest cannon opened up and fired at her, sending her right into the arms of a soldier. It held her down against the ground and gave a shrill screech into her ears. " **Your fight has been over for a while, Saturn Girl** ," C.O.M.P.U.T.O taunted her, " **it is time to join your comrades**."

The soldier over her took its other hand and formed it into a laser. It placed it against her head as it began to glow. Kel-el turned her way, only for Imperiex to pin him on the ground and hold him down with his foot. "She is only the first of many, Kel-el."

* * *

"Stop this, Brainiac," Querl couldn't look away as the computer screens zoomed in on Saturn Girl, about to be shot, "don't hurt her!"

Brainiac 6 didn't reply, silent as he watched the screens, backed turn to his ancestor.

"Listen to me, you don't have to involve them! _Face me_!"

"…Once we are connected, everyone will be involved," Brainiac finally turned to him, "until their time comes, and we download them into our programming. For eternity."

"You're obsessed with this idea of control that you seem to think I need to be a part of," Querl had nothing else but reasoning on his side, "but for once in your life, can't you admit that you're wrong? You can't keep order in the universe forever."

Brainiac 6 said nothing again, turning away to the screens. The robot soldier was done charging, and Querl could do nothing as it readied to fire down on Saturn Girl.

To start the nightmare all over again.

 **Dun-dun-DUUUUUUUUUUUHHHHHHHH! Things are getting a little too hairy for the Legion's comforts now. Yeah, so we can all thank Brainiac...6 for the unwarranted invasion of New Metropolis. I mean, I'll be honest, he did sort of just show up in the second season of the show, and suddenly began taking over Brainy, thus stealing the spotlight from the main villain of the series that far...but he's also really cool and menacing, and Imperiex was still...you know, there, so...all's well that end well, right?**

 **Until the next chapter!**


	10. 10

Time seemed to be frozen. Kel-El watched as Saturn Girl closed her eyes, one of the robots of C.O.M.P.U.T.O readying to fire at her head. Imperiex sneered. "Finally ridding us of that weak shell."

" **For father**."

"No," Kel-el tried to remove Imperiex's foot, "don't!"

The robot looming over Saturn Girl pushed the laser against her cheek. She shut her eyes, awaiting the attack.

 _Whoosh!_

The laser tore through the concrete ground, penetrating it until there were cracks reaching out a few feet. The robot stepped back to find the legionnaire had disappeared. It looked around but found nothing. " **She has vanished from my view**."

"Keep up, C.O.M.P.U.T.O – ha, like you ever could!"

Kel-el recognized the voice. From behind the robots zipped out a young black girl in a ponytail and blue and white jumpsuit. She gave them a big smile. "Good thing I decided to take my ring off when it stopped working, huh, Imperiex?"

"You may run fast," the warrior warned her, "but no amount of speed will be able to save you."

"I'm not the one who'll need saving. Now, Blok!"

Kel-el felt Imperiex's foot lift off him as a large figure made of stone, in blue shoulder pads and boots, yellow wristbands and a body suit, lifted the warrior off and tossed him away, his swords skidding out of his reach. Blok helped Kel-el up. "We seem to be the last legionnaires in the city. XS, where did you place Saturn Girl?"

"I'm right here," Saturn Girl ran back to them beside XS, "there's no need to remove me from the battle quite yet."

"Cosmic Boy and Lightning Lad are always on my case about keeping you safe, though." XS sighed. "If you're injured, I'm in trouble."

Blok pointed in the direction of the Legion's tower. "It will be easier to confront Cosmic Boy once we've saved him and the others from C.O.M.P.U.T.O's hypnosis. Kel-el, can you and XS get us there before Imperiex?"

Kel-el glanced at the warrior who was collecting his swords. "So you would run, then?" Imperiex faced him. "Make your choice, Kel-el – perish with your allies, or fight me to the death for the honour and glory you know you deserve."

"…There's no honour is letting my friends die." He grabbed Blok and raced off, XS and Saturn Girl close behind as she ran circles around Imperiex. They were out of his sight in seconds.

"…So be it. C.O.M.P.U.T.O," he called forth all the robots in the area, "commence phase four. We head for Legion headquarters, and at last end their pathetic reign!"

* * *

"…I'm guessing you guys aren't much for conversation?"

Supergirl gave the robots a weak smile, but they had no response. "…Could you at least turn your heads a little? Your staring is starting to freak me out."

She had been standing in the kryptonite glass tube for too long: her legs were beginning to cramp up on her. The soldiers did nothing but stare and hold their arms behind their backs. She had no means of escape, nor a plan for when she did.

"So this is what Kal was protecting me from," she murmured to herself, "boy, am I in over my head. If I don't find a way to get out of here, him and all his friends are going to suffer the same fate Krypton did…?"

Sparks were flying from the left robot, and it crumpled to the floor. Before the right one could react, some invisible force knocked it against the wall and pulled out a wire from its neck, immediately shutting it down. Supergirl watched in amazement as a young girl unshrunk herself before her eyes. She had pale skin, short black hair that matcher her leggings, and a green and purple dress on. "Sorry I'm late, Supergirl."

She walked over and took to the console. In a few seconds the kryptonite glass tube vanished into the ground, and Supergirl broke the wires around her. "Better late then never, uh…"

"Shrinking Violet, and don't worry, I didn't come alone. The coast is clear, Invisible Kid."

A black boy in a yellow suit and headband adjourned by a white exclamation mark phased into visibility. He held her hand as she stepped off the platform. "Good to see you're alright."

"How did you two not fall under C.O.M.P.U.T.O's control?"

"My ring was in for repairs when the tower came under attack, and Violet here was having hers upgraded."

She snorted. "I want a bright pink flashlight addition. Hope you don't mind the company, Supergirl. I know you're probably more than fine on your own, but-"

"No, no, no," she held her hands up, "look, whatever I'm to become, this great hero in the future – that's not the current me! I have no idea what I'm doing, and Brainiac, the robot that destroyed my planet, is here, and…and…I have nothing."

Invisible Kid put a hand on her shoulder. "You're not a great hero because you always have a plan, Kara. You went down in history for your charisma, bravery and leadership. Brainiac has nothing on you."

"…You think so?"

"And you're _not_ alone. There might only be three of us, but just think: once we rescue Brainiac 5, we'll have a whopping _four_."

Violet snorted again, and Supergirl felt her confidence returning. "Super strength, shrinking and invisibility? Easy."

"Really?"

"If I question it, I'll starting having doubts, so let's go before that happens." She led them out into the ship corridor, where they looked either way for more robot soldiers. "We find Brainiac 5, we find Brainiac."

* * *

"You gotta be kidding me!" XS smacked her forehead. "So much for speed."

They had made it to the tower to find their fellow legionnaires inside glass cases up the walls, but they couldn't stop the robots from collecting overtop the building. They were joining together and forming some large laser pointing down at the tower. "I thought Imperiex wanted to crush us one by one?"

" **It is nothing more than a precaution**."

"C.O.M.P.U.T.O," Blok awed as the tower-high robot walked out from behind the tower, "what is this?"

" **Yet another choice, if your simple minds can handle it. Stay out of the way – or watch your tower be obliterated**."

 **I don't really know how Brainiac could use C.O.M.P.U.T.O to do all these things with New Metropolis technology...but screw it, if the real show can have tiny plotholes, then so can I! It's more fun that way sometimes. And yes, I've included Invisible Kid in the story because he's cool, and now Supergirl is on the ship with the nerd trio. Time to save the world!**

 **Until the next chapter!**


	11. 11

The laser was finished, and it was _huge_. Kel-el thought about flying up and taking it apart, but Saturn Girl shook her head. "I know what you're thinking, but we can't risk it. If the laser fires before you can destroy it…"

"I know." He clenched his fist. "C.O.M.P.U.T.O, where's Brainiac?!"

" **Preparing for phase two of Brainiac 5's transformation. You will not be dealing with him**."

"You will be dealing with _me_."

They turned as Imperiex floated towards them, swords at the ready. "You had your chance for a true battle, Kel-el. Now you all face the edge of my swords. So, who's first?"

XS cracked her fingers. "Dibs." She ran round and round Imperiex. "Slice me if you can, bozo!"

Imperiex smirked. "C.O.M.P.U.T.O."

C.O.M.P.U.T.O aimed its hand at them, and from it shot out a shockwave that hit XS, slowing her to a halt. "Whoa," she rubbed her eyes, "I'm so…sleepy…nap time." She fell to the ground and started snoring.

"I may be proud of my power," Imperiex gently placed a sword next to her neck, "but I've wasted enough time with such nonsense."

Saturn Girl hit him back with a small mind blast, but C.O.M.P.U.T.O reached down and grabbed XS before they could reach her. It placed her inside an empty glass case and shut her inside. " **And then there were three**."

The three legionnaires stood side by side as Imperiex and C.O.M.P.U.T.O faced them. Kel-el brought his yellow knuckle shields out again. "If we're going to stop the laser, we need to bring them _both_ down."

* * *

"Too many years have you given your life to these pests," Brainiac 6 had seen enough on the screens to know the outcome, "you should be thanking me for saving you from such a terrible fate."

Querl was growing impatient. "I've seen enough."

"Have I convinced you of their incompetence?"

He looked his ancestor straight in the eyes. "Not theirs."

The doors to the room opened, and he was shocked to see Supergirl float in, gazing around the new area. "Man, this place is bigger than I had thought…Brainiac 5, you're okay!"

"Supergirl, you shouldn't be here!"

She locked eyes with Brainiac 6. "…You…must be Brainiac, then?"

"And _you_ are lost, Kara Zor-el. You should have stayed inside the city I collected from your dying planet all these centuries ago."

"…This is it?" She groaned, rolling her eyes. "I can't believe, after all these years, I've been so afraid of…of…a _toaster on legs_!"

"Kara-"

"Are you kidding me?" She gestured to him before glancing Querl's direction. "He's nothing without his skull ship. Look how tiny he is!"

Brainiac 6 gave her a moment to catch up. Then he shifted his body, expanding until he was twice her height and ten times bulkier.

"…I liked tiny."

"For all the times you placed errors in my plans," Brainiac 6 stepped towards her, "I must repay you, Kryptonian."

Querl felt his throne flatten out under him until he was laying across it, a metal clamp holding his neck down. Needles and lasers popped out of the metal, all aimed at his body. "Your technological metamorphosis can wait no longer. I will deal with the intruder while you are reconstructed."

"I don't mean to pressure you," Querl turned his head away from the needles, "but I'd rather not be tinkered with!"

Brainiac 6's arm stretched out, slamming Supergirl into the wall. She countered by grabbing it and racing out into the corridor, dragging him out of the room behind her. Querl heard whirling from inside the flat throne, and the needles started moving over him. He tried squirming but the metal cuffs only clamped down tighter. "Can I get a second opinion before this operation?!"

"I've got one," a small voice came from under the throne, "how about we hold off until further assessments?" Shrinking Violet flipped up onto the metal beside his head, smiling. "Unless you'd rather wait for a real doctor?"

"At this moment, you're better than any doctor in the world."

She snorted before shrinking down and jumping into the throne. The needles were an inch off his skin before something ripped them off. A hand phased into existence and gave him a thumbs up as his metal cuffs clicked open, letting him sit up. He rubbed his wrists as Invisible Kid and Violet joined him off the throne. "Looks like I've dragged the galaxy right back into my family problems."

Invisible Kid shrugged. "We've all got our quirks."

"An interesting discussion for after we save the world…hopefully. You can turn invisible?"

"Hence being called Invisible Kid."

"Follow Supergirl and make sure Brainiac 6 doesn't destroy her. Shrinking Violet, you and I are going to a bit of hacking."

Invisible Kid hid from their sight before leaving the room. Querl ran over to the main console to find the legionnaires on the screen fighting a losing battle. "Kel-el, Saturn Girl and Blok aren't going to be able to hold on against Imperiex and C.O.M.P.U.T.O for much longer. Not on their own."

"Good thing they aren't on their own," Violet stood beside him, "they have us."

"If we can hack into my ancestor's files and override the corruption on C.O.M.P.U.T.O, we should be able to free the rest of the Legion from its mind control. Can you locate its firewalls and reroute them?"

"You even need to ask?" She shrunk down and disappeared in between the buttons as he began searching through the ship's database.

" **Commencing laser preparations for emergency use** ," C.O.M.P.U.T.O spoke through the speakers, " **please place required code into system to activate**."

"I've got a code for you," Querl typed into the computer, "but it won't be ending with any activation."

The screens flickered as C.O.M.P.U.T.O's voice was thrown off balance. " **WhErE sHaLl We SiNg By ThE mOoNlIgHt, WhEn ThE dAy Is DoNe**?"

"Sorry, old friend," he pressed the flashing red button, "but the Legion comes first."

The screens went blank. "Let's just hope this works…for all our sakes."

 **C.O.M.P.U.T.O has always been a cool concept to me. A program that knows everything about the Legion, and only years after it's formed does someone thing "hey, what if I, you know, took all that important intel for myself, thus learning everyone's weaknesses?" Sorry, Emerald Empress, finders keepers when it comes to the defeat of the Legion. Now let's just hope Brainy knows what he's doing. Three years of travel can really mess with you...**

 **Until the next chapter!**


	12. 12

" **Laser preparing to fire**."

"C.O.M.P.U.T.O!" Imperiex faced the large robot as the laser above the Legion tower began charging. "You said I could destroy the Legion by my own hands!"

" **It was Brainiac 5 that activated the laser. He has made his decision, and I for one will not question him**."

"He did _what_?!"

"I don't believe it," Blok held Imperiex's swords by the ends as the warrior tried to push them towards his chest, "Brainy wouldn't do such a thing."

" **It matters not. Detonation of Legion headquarters in t-minus thirty seconds**."

Saturn Girl spun around. "Kel-el, now!"

He raced up to the laser, hoping to smash through it. However, as he neared the metal it lit up in dark red, momentarily blinding him. He felt his strength quickly drain from him as C.O.M.P.U.T.O stretched its arm out and slapped him back to the ground, creating a small crater. "Ugh, I won't be touching that anytime soon."

" **T-minus twenty seconds**."

"I have strength for one more mind blast," Saturn Girl tried focusing on the laser, "but I can't reach it from here! I might hit some of the legionnaires!"

"Hit some or lose them all, Imra!"

Imperiex shook Blok off and whipped his swords at the laser, but C.O.M.P.U.T.O smacked them aside. " **T-minus ten seconds**."

"I was to have my revenge! Brainiac and I made a deal!"

" **As you did years ago. Only a fool allows himself to be played twice over** -!"

Everyone gawked as the laser tilted away from the tower and aimed at C.O.M.P.U.T.O. " **The laser – what is happening-NOOO**!"

The laser fired, tearing through C.O.M.P.U.T.O and causing it to implode. It fell to pieces beside the tower as the robots separated, their red glowing ceased. Kel-el activated his heat vision and tore through a few at the bottom. "Saturn Girl, can you wake the others?"

"I'll try, but let's get inside first."

" **Impossible** ," C.O.M.P.U.T.O's eyes faded off, " **this is an…error…** "

Imperiex faltered on his legs and fell over. "What's happening…my systems are shutting down?!"

"C.O.M.P.U.T.O was the only thing keeping you from lying in space," Kel-el stepped over him, "where you belong."

"I am a conqueror. I won't be defeated by a faulty program!"

"…No, you won't."

Kel smashed his fist through Imperiex's chest, permanently shutting him down. Then he turned to Saturn Girl and Blok.

"Let's get to the top of the tower and save the rest."

As the others entered the tower, Blok scanned the skies, robots splitting up and going ballistic without C.O.M.P.U.T.O's instructions. "…Where does that put Brainy?"

* * *

"Are you sure you programmed the laser to target C.O.M.P.U.T.O and not the tower, Brainy?"

Querl ran through the hall corridors, Violet right behind him. "C.O.M.P.U.T.O moved his main circuitry to the cruiser, and I set the laser to only fire when it sensed its source. The others will be fine for now – at least until Brainiac 6 finds out."

"Why did Brainiac wait so long to return?"

"He was waiting for me to come home."

"Your home is Colu."

"It was…until I was banished for overriding the locks and firewalls on my ancestral programming and releasing Brainiac."

She gave him a sad smile. "Good thing you have the Legion, huh?"

"…I-"

 _Wham!_

Both fell back as something hard and invisible knocked them to the floor. Invisible Kid phased into view as they shook their heads. "Sorry about that. Brainiac didn't see and swatted me back with his leg."

"Wait," Querl looked ahead, "so Supergirl's facing him alone?!"

* * *

Supergirl hit the wall and cracked it up and down before balancing herself out. "Okay, so you've got an alright handle outside of your ship."

Brainiac 6 had seemed to have grown even larger as he approached her. "I have upgraded since the last time I saw you, hundreds of years ago. This could have been so much easier had you stayed inside Kandor."

"Forget it, I'm over my fear of you. You're nothing but a big robot that likes to think it's better than everything else, but in reality," she gave him a smirk, "you couldn't beat a broken blender."

"How childish." He shot a beam her way, but she zipped out of range and behind him. Grabbing his neck, she smacked him against the wall and up to the ceiling, letting him drop. "I may be childish, but at least I know my own strength."

"I know many things," he rose and faced her, three green circles appearing on his chest, "including the pinnacle of your weaknesses."

"Seriously? How can so many people have access to so much kryptonite?!"

"Supergirl!" Violet, Querl and Invisible Kid ran in beside her. "We totally owned C.O.M.P.U.T.O!"

"Intruders," Brainiac gave a quiet sigh, "how pressing."

His Kryptonite fired at them, but Querl held his arms out, forcing a force field in front of them and deflecting the shot. "Ah," Brainiac said, "my old shield programming. So you still have parts of me coded in your genetic constructing."

"Just enough to let me deal with you accordingly."

Shrinking Violet vanished. "Wait, no," Querl looked around for them, "Shrinking Violet, don't touch him!"

Brainiac 6 noticed sparks beginning to fly from his right arm, and he flexed it up. It glowed a deep green, and Supergirl could hear someone scream inside it. "Shrinking Violet!"

Violet flew out at regular size and fell to her knees. "Fool," he stepped behind her, "no one can hack into me. My programming is impenetrable."

He smashed his fist down over her, but hit only another force field. "No more," Querl cried out, "no more hurting my friends!" He whipped his arm out, and from it flew out a long force field in the shape of a larger hand that slammed Brainiac 6 into the opposing wall.

Supergirl took a deep breath. "Hold him while I finish this off."

Before anyone could move, the ship started beeping through the speakers, and red lights flashed from the ceiling. "Guys," Invisible Kid said, "either we're about to have a rave, or this ship is going down!"

"Indeed," Brainiac 6 admitted, "and from this trajectory, we'll obliterate half of New Metropolis in minutes. Say goodbye to your…friends."

 **Four chapters in one day. I don't think I've ever posted this much in one day, but I've already finished the story, so why not? And now Brainiac's pulled out the big guns - or should I say, big ship. And man is it fun writing Supergirl into this universe. I loved her in the Legion comics and I loved her in the Justice League animated series and animated films, and now I get to blend them all together into one entity. The ultimate Supergirl!**

 **Until the next chapter!**


	13. 13

Phantom Girl could feel something in her mind, a soothing voice that broke through the constant static drowning her senses. " _Listen to me, legionnaires. C.O.M.P.U.T.O has been defeated, but his robots are still here, and they're going to take out New Metropolis if we don't stop them. Phantom Girl, we need you to lead us_!"

She could see and hear everything now, and she found herself in a class case. Her flight ring was back on, and as she phased through the glass, she found the others waking up from their trances as well. She also found hundreds of robots in the sky. "Whoa."

Kel-el flew up beside her, along with Timber Wolf and Shadow Lass. "Okay, leader," Shadow Lass pointed to the skies, "an order as soon as possible would be splendid."

The whole Legion was facing her, waiting for her call. "…C.O.M.P.U.T.O was our program," she spoke loud enough for them all to hear, "so it's our job to clean up its mess. I have only one order."

She glanced at C.O.M.P.U.T.O's left over scraps, the remains of their cruiser, before giving a big smile. "Have fun!"

She then gestured to the robots that were turned their way. "And take them out!"

The Legion split, and a huge battle grew over the tower. "Colossal Boy, Kel-el, Superman, protect the tower! Saturn Girl, Timber Wolf, Dawnstar, keep civilians from getting too close! Dream Girl, Chameleon Boy, XS, take care of any straggler robots around the tower!"

Colossal Boy grew until he was as tall as the tower. "Has anyone seen Violet? I can't find her!"

"Kara's missing, too," Superman threw two robots into another three, "as is Brainy."

"Superman," Lightning Lad tried to break the news softly, "Brainy's been gone for years."

"He was here, moments ago."

"… _WHAT_?! And he didn't even bother to say hello?"

"Uh, in his defense," Triplicate Girl kept kicking, "The city was being overrun by a computer that thought he was its father."

"…Point made." Lightning Lad's scar glowed, and he blasted two dozen robots surrounding him out of the way with his electricity. "…Wait, his _father_?"

"Okay, yeah," Bouncing Boy bounced up next to him, "can we talk about how unnerving that is?"

"Superman is right," Karate Kid and Wildfire were back to back, "Supergirl and Brainiac 5 are missing, and I cannot find Invisible Kid."

"Newsflash, Karate Kid, he can turn invisible. Makes looking for the guy tough."

"We'll deal with finding the other legionnaires later," Cosmic Boy and Star Boy crushed robots together into a huge clump and dropped it on top of others, "first let's get rid of these robots and clean the city up!"

Kel-El glanced at Saturn Girl. "Brainiac is here, and you didn't bother to tell Phantom Girl?"

"We need her to be calm while she leads the others," Saturn Girl pointed to another cluster of civilians, "Dawnstar, search this area for others while I calm these people."

"I can sense more by the shopping district" she replied, "I'll guide them away from the tower." As she flew away, Timber Wolf gave a deep growl.

"If Brainiac is here, Kel-El, Brainy's disappearance makes a lot more sense."

Saturn Girl took a moment to speak into the minds of the people. " _The Legion is here. You have nothing to fear now. Please calmly direct yourselves to the safe zones. The Science Police will take you from there_ …We have to have trust in Brainy," she told them aloud, "and Supergirl. They can take care of themselves."

* * *

"Okay," Invisible Kid was yelling now, "is it just me, or is the alarm getting louder?"

"The ship will crash into the planet's side and destroy everything in the vicinity," Brainiac 6 was still against the wall, Querl's force field hand holding him back, "and only C.O.M.P.U.T.O can stop it."

Violet and Querl shared a regretful look. "Of course it is."

"Okay, Brainiac," Supergirl flew over to him and held his fist by his face, "either you stop this ship, or I punch your face into the next century. If you think I'm going to believe that you can't stop this, then you've clearly underestimated me."

"I have no reason to stop this. Once I have the ability to digitize, it won't matter what sort of impact occurs. All information will be mine."

"You mean ours," Querl ruefully reminded him, "since you can only do that with my brain attached to yours."

"Which is never happening," Supergirl summed up, "so we're back to square one. Stop the ship or I bash your brain in."

"You are not a threat to me, Kara Zor-el."

"…Invisible Kid, Shrinking Violet, try to slow the ship down from the main console. Find anything you can in its system, and be quick about it!"

"Got it!" They flew out as Querl tightened the field hand around his ancestor. He glowered at his ancestor.

"If you won't do anything, we'll stop the ship. I won't let you do any more harm, Vril Dox."

"I do not wish to cause harm," Brainiac was repeating himself, "only to bring order to this flawed, chaotic-"

"Enough! You know I never meant a word of what I said back then!"

"Brainiac 5!"

He fell silent as Supergirl looked him in the eyes. "If you can't keep your emotions in control, then go help the others. You won't be able to help me if he gets inside your head. I know your emotions are still new to you, but if we don't do this your friends will die."

"…Right. Sorry."

"No more talk from you, either," she turned her attention back to Brainiac 6, "except for telling us how to stop this ship."

"You will have to catch it, Kara. There's nothing inside here you can accomplish."

"We can turn the ship off!"

"The ship is already off, thanks to the work of Brainiac 5." His gaze fell to Querl. "The price of human emotions is pride."

"Hey, brain bot," Supergirl wretched his head back towards her and leaned in close to his face, glaring, "you're speaking to me and me alone-"

 _Boom!_

Smoke billowed out from the corridor. "Supergirl," Querl's force field hand wavered, "Shrinking Violet and Invisible Kid are down there!"

 **Tensions rise as Supergirl takes the lead in a desperate attempt to stop the ship from crashing into the city and destroying their friends. And who doesn't like random explosions putting characters in more peril, right? Oh, and if anyone was wondering why I made Phantom Girl leader...screw it, she deserves a chance just like the rest of them! I love her character, and she's more than ready to take the lead!**

 **Until the next chapter!**


	14. 14

Supergirl eyed the door where smoke was pouring out from. "Querl, find them before- _ugh_!" She felt Brainiac 6 wrap his neck around hers, his head resting over her body as he tightened. "Go!"

Querl faltered before nodding. His force field hand vanished and he ran through the door, leaving her alone with Brainiac, who leaned in beside her ear.

"The ship falls apart as we speak. There is nothing more you can do besides joining Kal-el on Earth."

"I can handle this. I don't have to defeat you – I only have to make the ship falling as bad for you as it is for us!" She grabbed his neck, unraveled it and wrapped it around a pipe sticking out from the floor. She tied it into a bow and smiled. "…It suits you."

"Further proof that you are still a child." Brainiac 6's body walked over to the neck and quickly untied it. "I do not play games, Kryptonian."

* * *

"Vi! Invisible Kid!" Querl held a force field over his mouth to keep from inhaling too much smoke, but it didn't help with his vision or hearing, the blaring red lights and siren still going and growing louder by the minute. "Can either of you hear me?"

He found the source of the explosion to be the main console room, and as he ran in her felt something nudge his shoulder. "Invisible Kid?"

"Here," he heard him cough hard in his arm, "but I lost Violet."

"What happened?"

"We tried to work the console, but it blew up in our face. Some sort of firewall left over from C.O.M.P.U.T.O. We have to get back to Supergirl."

"We have to find Violet first." He tried to step forward but a hand held him back by his arm.

"Brainiac 5…I'm sorry…Violet was inside the console when it blew."

For the first time, Querl felt everything go cold. He had known death as a robot, and he had heard some terrible stories on his travels the past three years, but he had real emotions, and they were currently screaming guilt into his eardrums and shoving it down his throat. He could feel Invisible Kid tugging at his arm, but he didn't move.

"…She…she can't be…"

"Brainiac 5, come on, there's nothing else we can do!" He appeared through the smoke, eyes dark. "I tried to stop her, but…we need to go."

"…Go without me."

"Brainiac-"

"I'll join you soon, I promise."

Reluctantly, Invisible Kid exited through the corridor, covering his mouth with his hand. Querl felt his way to what remained of the console and began to search through the blown metal and wires.

"Come on, Vi, where are you?"

He didn't know how small she was or where she had ended up during the explosion, but he _needed_ to find her.

The smoke was thickest around the console, however, and was spreading over him. "I can't leave," he murmured, determined to find some trace of Violet before leaving, " I can stay…I can-" He broke into harsh coughing that made his lungs sore. "I can't leave…?"

The smoke suddenly seemed to vanish from his mouth, and it no longer stung his eyes. He looked himself over to find a light purple glow covering his entire body. "…My force field…it's protecting me…like blood cells! It reacts when I'm in danger…half the time."

"…Brainy…"

"Violet!" He knelt down and ran his hand over burnt wires, feeling no pain. Finally he found a small figure hidden underneath a metal plate and wires melted together, and gently picked it up. He held her close to see her covered in cuts and scrapes, barely able to sit up. "Violet…"

She gave him a weak smile. "Sorry…we couldn't…shut it down…"

He had to use all his willpower to keep from looking away. "This is why I can't return to the Legion. I'll only end up hurting everyone again, and sooner or later I'm going to start something that I won't be able to undo!"

"We all bring something different to the Legion, Brainy," Shrinking Violet comforted him as best as she could in her condition, "good and bad. No one blames you for Brainiac."

Querl could see how painful it was for her to speak. He placed a force field around her to keep the smoke out before standing up and turning to the door. "…I blame myself for Brainiac."

"Don't."

"Its fine," he gave her one of his most serious expressions, "I'm not going to hide from him. Not anymore."

* * *

Supergirl waved the smoke away. "Lost him again. Show yourself, Brainiac!"

"Supergirl, over here," Invisible Kid was next to her, "we have to get off this ship before it hits the city and blows. Brainiac was right about one thing – there's no stopping this ship from the inside."

"If we leave Brainiac will escape."

"There will be other chances to-!"

A dark green arm wrapped around him, and he was sucked back into the smoke. Supergirl tried to follow, but her senses were in disarray. "Brainiac!"

"I told you, I do not play games."

She heard Invisible Kid yell out before hitting the ground next to her, unconscious. She turned to him, only for two fists to hit her stomach and throw her against the wall. Before she could get her bearings, another blast of green energy hit her, knocking her head back. She flew around, using her x-ray vision, but electric shocks ran through her body as a pair of hands clapped her back.

" _Ahh_!"

She fell to the floor as Brainiac 6 stood over her and Invisible Kid's bodies. "I grow tired of your extensive and useless fighting." He raised his arm, where a laser cannon formed and charged up. "I won't be needing your data. A deletion is required."

"Brainiac!"

Brainiac turned as Querl stepped out, Shrinking Violet in his hands. He gave him a cold glare before gently placing her down beside Invisible Kid, then stood toe to toe with Brainiac.

"This is _our_ fight."

 **Alright, it's Brainiac vs Brainiac once again! This way I can give the guy a physical fight against his ancestor, instead of him calling on four...fiery...other consciousness'? Yeah, I never got what really happened in those last few moments of the series, but it was totally cool none the less.**

 **Until the next chapter!**


	15. 15

"You would fight me for them?" Brainiac gestured to his unconscious friends on the ground at their feet, though Supergirl was stirring. "I offer you immortality."

"You offer me emptiness and destruction."

"We would control everything."

"No, _you_ would control everything. _I_ would be forced to watch you hold trillions of lives in your mind for pleasure. I won't be a part of your order."

"…Then I leave you with no choice." He grabbed Querl's neck. "And no humanity."

Querl didn't respond with words. He reached into his cargo pocket and pulled out some loose wires attached to a sharp circuit board edge – and rammed them right into Brainiac 6's eye. As his ancestor gasped and stepped back in surprise, letting him go, he reached down, grabbed a loose pipe rolling along the floor, and with one swing knocked Brainiac into a stumble.

"Ugh," Supergirl sat up in time to see Querl ram Brainiac into the wall with his force field hand, "…Brainy?"

Brainiac was impressed, despite the sparks rolling out of his damaged eye where the circuit board edge stuck out. "You have real anger now. Does your mind feel any clearer?"

"Thank to Supergirl."

She kept silent so he wouldn't notice her listening.

"She was right. I can't let you into my head. You're physical now," he smirked, "and while that means I don't have as much control, it does mean I get to let off a little steam. Supergirl."

"…Huh? Oh, right!" She stood and started towards him until he held his free hand up to stop her. "What?"

"Take Invisible Kid and Shrinking Violet to the tower and stop the ship with Superman and Kel-el."

"…What about you?"

"I'll keep Brainiac here. Go, before the ship hits."

She wanted to argue and bring him with her, but she also knew that there was no way she could make that choice for him. She didn't know him like her cousin or the others did. She was an outsider, even if they knew her from the archives, and she had to be the leader they had come to admire.

"…Don't be too long."

She placed Invisible Kid over her shoulder and carried Shrinking Violet in her hand. With one last look at the Brainiac duo, she vanished with super speed. Querl hadn't taken his eyes off Brainiac 6.

"If this ship falls, you fall with it."

"As will you, in due time."

* * *

Superman knocked another robot away from noticing a figure flying towards him. "Kara!"

She hovered down in front of him and handed Invisible Kid and Shrinking Violet over to Blok before giving her cousin a big hug. "I was so worried about you, Kal."

"And I you," he squeezed her tight before holding her back and checking her over, "but what happened to you? Where have you been?"

"Poor Violet," Blok commented, "you've recently been in a fight, all of you."

"It's Brainiac, but we've got no time," She saw Kel-el out of the corner of her eye, "Kel, over here! We need to stop a ship from destroying New Metropolis and killing Brainiac 5 in the process!"

He turned her way, eyes wide. "Uh, what?"

She pointed to the sky. Chameleon Boy was close by, and as he looked where she pointed, he made out a large object on fire descending towards the city. "I'm guessing that isn't a wishing star passing by to give us luck!"

Karate Kid nudged him. "Very deductive."

"We have to slow it down," She glanced at the Kryptonians, "and hopefully _before_ Brainy roasts in the descent through the atmospheres."

"Wait," Superman touched her arm, "Brainy is on that ship? With Brainiac? Falling to their deaths?! We have to get him out first!"

"He made his choice, Kal. We had to leave him-"

"You left him on purpose?!"

"He can take care of himself, Kal!" She turned to him, frowning. "I know I don't have your experience or expertise, but I know when to let people make their own decisions. We each have our own battles, and Brainy's is up on that ship. Our fight is making sure there's a chance he can come out of that fight alive."

Kal and Kel stared at her, blinking in silence. Then they both gave her a reassuring smile. "…I see," her cousin pulled her close, "maybe I have been too protective."

"Yeah…how about we make up fully _after_ we've won."

The trio joined up and tried to fly off, only for more robots to block their way. "Really?"

"Oh no you don't!" Cham transformed into a giant dragon and cooked them with his fire breath, melting them away. "Go, you guys!"

* * *

Querl placed his hands over his face, deflecting Brainiac 6's laser with his personal force field. "You can't penetrate it, Brainiac. It's your perfect creation."

"Placed within the imperfections of your organic body," he replied, "there will without a doubt be an error in its mechanisms."

"It no longer has mechanisms."

"Exactly." He grew into his larger battle mode and dove at Querl, who barely dodged out of his way. "You are an unimaginable intelligence trapped inside such a fragile, organic sack."

Querl looked up just as Brainiac 6 backhanded him into a boiler, where he slid to the ground. The boiler, a little bigger than himself, shook free from its holdings and fell on top of him, pinning him to the ground. He tried to move but couldn't free his legs as everything was growing hotter.

"You made this decision," Brainiac 6 reminded him, "and now you face the consequences."

"So," he gasped, "you'll let me die, and lose your one way of digitizing the galaxy?"

"You misunderstand. You chose to fight me knowing you may die. I chose to allow this, knowing that when you were defeated, you'd have no way of fighting back."

Querl felt embarrassed, angry and scared. Brainiac 6 freed him from the boiler. He tried to run, but was quickly grabbed by one of his large hands.

"You would run?"

"Not from you," Querl looked behind them, "from _that_."

Large flames were erupting in the ship, and soon they would overtake the entire cruiser.

 **Drama! Action! TWO BRAINIACS! THREE KRYPTONAINS! This story is coming to an end in the next few chapters, but not before the Legion attempts to save New Metropolis from a crashing ship and the left over robot soldiers. Can Supergirl possibly help her cousin and his clone stop the ship from crashing and taking Brainy down with it?**

 **Until the next chapter!**


	16. 16

"I will teleport us now."

"Teleport?" Querl watched a new button his Brainiac 6's belt open up. "To where?"

"You think this is all I've prepared for us?"

"…Wait," he didn't want to ask but had no choice, "are you saying you've been forming an army elsewhere?!"

"Far beyond the Legion's reaches, and far greater than Imperiex's. He had limitations – I have none."

"You aren't unstoppable," Querl struggled against his grip, "and you aren't a god!"

His force field expanded, breaking him free of Brainiac 6. He focused the energy into his fist, and as he swung it up, the large force field hand came out in a fist, plowing into his ancestor. He flew back and into the flames, where Querl could hear him tear apart. A sound he never thought he'd hear, like metallic velcro, and it made him more uncomfortable than the increasing heat.

 _Slam._

The doors before him shut. He tried prying them open but they wouldn't move. "The ship's locking down. It's preparing to self destruct." He looked around for another exit, but there was too much smoke and fire.

"…So," he gave a sad smile as the flames reached towards him, "perhaps now I've been redeemed."

* * *

"Here it comes!"

The ship was in flames, soon to reach the tops of the highest New Metropolis buildings. Supergirl led the other two forward, over the buildings and into open air. "It's coming at us sideways. Kel-el, take the back. Kal, hold the front. I'll slow it down from its side. Watch out for the flames."

Kal-el was becoming more impressed with his cousin by the minute. They flew off in their directions and soon faced the ship head on. He blew the flames away with his ice breath and grabbed the ship, which shoved him back. It was speeding up and the metal burned his skin, but he held his ground. Supergirl and Kel-el placed their hands against it, and as it neared the buildings they pushed back.

"Come on, guys," Phantom Girl watched earnestly from below, "hurry."

Finally, just when it seemed the ship was about to take the tops off the apartment towers, the three Kryptonians slowed it to a halt. Phantom Girl and other legionnaires sighed with relief before returning to the remaining robots.

"I'm not one to complain," Kel-el commented as the trio shared a relieved smile, "but isn't this a bit anticlimactic?"

Suddenly the ship began to hum, louder than before. It was glowing red now, and the flames were increasing.

"Me and my big mouth."

"It's gonna blow," Supergirl caught their eyes, "we need to get it as far away from the city as we can! Kal, quick!"

He stared at her as though she were an alien…that he didn't know. "We can't yet! Brainy's still in there!"

"Kal, please-"

"We have to find him!"

She gave him one last pleading look before realizing that he wasn't going to listen. She gave Kel-el a quick glance. "Kel-el, do it."

As he grabbed the end of the large ship she raced at her cousin, slamming into him and flying them back until they were out of range. She then held onto his arm as Kel-el swung the ship around a few times, gaining speed. With a yell he tossed it higher and higher into the sky as it was consumed by flames, until finally it-

 _BOOOOOOOOOOOM!_

"No," Superman cried out, "BRAINY!"

Triplicate Girl and Bouncing Boy looked up to watch as the ship exploded into a burst of fiery clouds of smoke and metal. It sent a minor shockwave through the city that shook them up but did no damage as scrap metal rained down.

"They did it," Wildfire gave a whoop, "the ship is down!"

"But," Triplicate Girl look around before hovering down beside Bouncing Boy, "where's Brainy, then? You don't think…," she could see Superman's terrified expression, "…oh, Bouncy, no, no!"

He held her in his arms. "I…I don't know…"

Meanwhile, the three Kryptonians couldn't take their eyes off the explosion as it began to settle. "…I'm sorry, Kal," Supergirl slowly flew into his view, "there's nothing we could have done…nothing _you_ could have done. If you had gone inside and the ship had blown…he made his choice, Kal."

"He's surprised us before," Kel-el tried to lighten the mood, "if we give it a moment…maybe…"

It took more than a moment for the smoke to clear, but there was no movement aside from the wind blowing the smoke apart. Superman lowered his head, and Supergirl felt like doing the same – until she saw the glimmer of purple energy phasing through the embers.

"Kal, look!"

He was breathing heavy and holding his left arm, but there was no mistaking Querl through the clearing smoke. The Kryptonians flew up to join him as he left the ship remains, his force field switching off. "Hope my ancestor was smart enough to get insurance."

"You're a real piece of work, you know that?" Kel spoke through a smirk as Superman gave Querl a big hug. "The last thing we need is a softie Superman on our hands."

"So," Supergirl spoke aloud her hopes, "Brainiac is gone now, right? I mean, he couldn't have survived that explosion without his-er, your shield."

Unfortunately, Querl shook his head. "I doubt he stayed behind. He has teleportation technology in his belt…but at least he knows now that it's going to take more than invading and threatening a planet to get me to join him."

"Brainy!"

XS and Lightning Lad flew up and hugged him as the others floated around, calming the citizens who cheered below. The robots were falling from the sky, unable to function without C.O.M.P.U.T.O and Brainiac's control.

Kel-el spotted movement at the tower entrance, and as he zoomed down, he saw a couple of Science Police placing Imperiex's body onto a stretcher for removal.

"…"

Triplicate Girl and Blok came up beside him. "So, how does it feel to have finally defeated your mortal enemy, Kel-el?"

"…I waited so long to fight him, and when I finally had the chance, he was nothing more than someone else's puppet."

Blok turned to him. "Would it have felt any better fighting him when he was completely in control, though?"

They watched as the body was placed into a collection truck, driving off to be disposed of.

"I would have felt empty." He gave them a smile. "Kinda hard to enjoy a victory without…you know, allies."

Triplicate Girl playfully punched his arm. "Friends, you dope."

 **And so, finally, Kel-el can rest easy, knowing that Imperiex is gone for good. Side note, I think I may have been spelling Kel-el's name wrong this entire time...but whatever, it looks cooler this way than with two L's. And Brainy has made it out alive! Now for the cool down sessions with the Legion, and possibly a little surprise for Supergirl...**

 **Until the next chapter!**


	17. 17

The Legion tower was in major need of repairs, but for the moment its heroes did the only thing anyone had the energy to do – relax and converse. They were all inside the building, checking over each floor in groups while discussing their latest experiences. Finally they all met in the largest room in the middle of the tower, and Supergirl felt as though she were at a quiet party. "No snacks. How sad."

"I could pick us up some Saturn burgers," Chameleon Boy made a quick stop beside her, "I hear they come with toys now."

She gave him a laugh. "I might take you up on that offer later, Cham, thanks."

He left to greet Dawnstar. She watched Shrinking Violet run and jump into Colossal Boy's arms and he spun her around. Cosmic Boy and Phantom Girl were off to the side, talking about Brainiac 6 and his mysterious, yet to be found army. For the time being, she was content with not dealing with the consequences of their fight.

"I'm surprised you're not the one being bombarded by questions."

Querl stepped up beside her as that stood out of the way of the rest of the group. She shrugged. "You're the one who left for three years. I'm just…Superman's cousin."

"You are more than that, Kara. You don't know it yet, but while Kal-el may become more well-known, you're still one of the most honoured heroes of the twenty-first century."

"Really?"

"I have a twelfth level intellect," he smirked, "I…rarely make mistakes."

They saw Lightning Lad being taken on either side by XS and Saturn Girl, who were bugging him about his desire to keep the latter safe. "…They've grown a lot," Querl's eyes fell to the floor despite his smile, "their safety is all I can ask for."

Supergirl knew what was coming next. "You're leaving."

"My first visit in three years, and I bring the end of the world with me again. Things will be better this way. Bouncing Boy already has my ring."

"I won't stop you," she glanced at Kal and Kel, "but they won't be happy."

"Will you be staying, Kara Zor-El?"

"For a while. I can't take Kal away from his friends, and it'll be great training here in the future with the Legion."

Querl held his hand out for her to shake, but she wrapped her arms around his neck in a hug. "Thanks for giving me the chance to prove myself to Superman."

He placed his hand on her back. "Thanks for not beating me up for being a Brainiac."

She let go, and he turned to the door. As he approached, it opened, and he nearly bumped into Dream Girl. "Oh, Brainy! Where are you off to?"

She had spoken too loudly, though Supergirl assumed she had done it on purpose. Now everyone was looking their way. Querl turned to face them, unsure what to say next. "I'm just off too collect my luggage," he averted his gaze, "from the passenger ship."

"Great," Bouncing Boy crossed his arms, grinning, "we'll send someone with you to help pick it up."

"It's okay, I can handle it…," he looked from face to face, "…you won't let me go alone, will you."

"No," the entire Legion replied in unison before breaking into laughter.

Wildfire draped his arm over Querl's shoulders. "The last time the Legion let you leave on your own, you left for three years. I wouldn't be surprised if they stick a tracking device in one of your teeth."

"Face it, Brainy," Phantom Girl nudged him, "you're stuck with us."

He sighed, his shoulders slumping. And then he did something that no one, not even Dream Girl, could have ever seen coming.

He laughed.

A real laugh.

"Good thing I travel light…what?" He noticed everyone staring at him, wide eyes and jaws dropped. "What'd I do?"

"…You," Timber Wolf pointed at him, "you laughed."

"…This is going to take some time, huh?"

"Which is why we have these ready." Dawnstar walked up with a golden box, and opened it to reveal two flight rings and two belt buckles. "Just make sure not to be giving these ones away, got it?"

"Neat," Supergirl examined them, "but why do you need two?"

Now everyone was staring at her. "Um…"

* * *

"You ready?"

Supergirl stood next to Querl in front of the entrance, the rest of the Legion standing at the bottom of the stairs. She had her ring and belt buckle on, matching with Querl's new yellow belt. "I hope so."

"Just repeat with me what Superman told you."

They held their hands up. "To the Legion of Superheroes, I make this solemn pledge. To use my powers for good, to fight for justice and protect the innocent. To aid my fellow legionnaires in times of peril, and to keep their secrets safe. I am – Supergirl!"

"Brainiac 5!"

Everyone held their rings up to the air. "Long live the Legion!"

As soon as it had finished, Supergirl flew down into Superman's open arms and gave him the biggest hug she had ever given. "…Do you think _he_ would be proud?"

An image of his dark, brooding friend a thousand years in the past flashed in his mind. "It'd take Saturn Girl's telepathy to drag it out of him, but next to me, no one could be prouder."

"Just remember," Shadow Lass looked her way, "you being Supergirl doesn't make you better than the rest of us."

Supergirl gave her a snooty look. "I understand. It'll be my strength, speed, charisma and skill that will make me the best."

Shadow Lass opened her mouth to say something, but she had nothing. She gave Supergirl one last look over before floating away. They left her to her own devise, turning as people congratulated Brainiac 5 on his return.

"So, think you can work with a Brainiac, Kara?"

"Easy, Kal. Besides," she shared a happy look with Querl, giggled and gave a lighthearted sigh, "he's way, way too cute to hate."

Kal and Kel shared their own look of utter astonishment and confusion. "…Cute?"

 **Yeah, I know in the comics Brainy had a relationship with Dream Girl, and the show had some hints of his feelings for Shrinking Violet, but think about how cute he and Supergirl could be! I'm all for it, sort of like the Justice League animated series. Only here, Kal's okay with it. Anyway, this is the penultimate, and now comes the finale!**

 **Until the next chapter!**


	18. 18

**EPIOLOGUE**

The planet was abandoned, not a soul in sight – save for the thousands of robots patrolling around the large ship field in the valley of rock and dust. Each wore armour with Brainiac's sigil on it, and all had advanced weaponry.

Inside the main ship, sitting at his throne, Brainiac 6 watched the screens. A blueprint of Brainiac 5's organic body was viewed beside the schematics of C.O.M.P.U.T.O. "So his humanity has taken over his sanity. I must find a way to…break it."

He pressed a button on his throne arm, and a video feed popped up before him. A hooded, masked figure sat in a dark grey room. "Brainiac, I presume. To what do I owe the pleasure of meeting your personal acquaintance?"

"I ask of you a simple request," he replied, "one that will provide for both of us a satisfactory payment."

* * *

"Can we really trust C.O.M.P.U.T.O as the Legion's security system and data collector after all that's happened?"

Brainiac 5 and Invisible Kid shut the main console down before turning the Legion's headquarters back on. The Brainiac sigil appeared, but this time it was smaller and a lighter grey. " **Welcome back, Brainiac 5**."

"It's a Cyber-cerebral Overlapping Multi-Processor Utilizing Transceiver-Operations, Lyle, and with Imperiex completely wiped from its database, there should be no major errors like before."

"You sure?"

"Positive. It's not alive, just a program I created to help keep information organized for us."

"You'll have to show me how to work this thing," Invisible Kid pat the console before exiting the room, "and Violet, too."

Brainy typed the few remaining codes into the system before sighing. He had decided to stay with his jumpsuit and pants, but that didn't make the work any easier. "C.O.M.P.U.T.O, reconfigure Legion headquarters to previous foundation."

" **Reconfiguring Legion headquarters. Estimated time to completion is two hours**."

"…It's good to be back," he finally admitted to himself as he walked out of the main console room, "I can only hope everything will slow down for a bit."

The doors closed behind him, leaving C.O.M.P.U.T.O with its command. The room was silent as the screens slowly faded into a loading screen.

"… **What is my purpose**?"

 **ROLL CREDITS**

 **You know, like a real cartoon would. Whelp, I did it. I wrote a season three I'm happy with. I currently working on a second episode to follow it up, and who knows, maybe I'll write more if people want them. Maybe someday I'll have an entire season to my name. It's nice to dream. Anyway, thanks for reading, and be on the lookout for my second episode, "Substitute Leader", hopefully coming soon. They'll be shorter than this one, because this story had two episodes in it, but I won't be holding back, trust me.**

 **Thanks for reading, and until the next episode!**


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